Re: [Bioc-devel] as.list of a GRanges

Hi Hervé and others, Thanks for the responses. I woudn't call as.list() of a GRanges an "obscure behaviour" but more a "works as expected, even if not clearly documented" behaviour. In any case I can change the code to as(gr, "GRangesList") as suggested. Thanks again for the responses and di

Re: [Bioc-devel] as.list of a GRanges

On 02/15/2018 01:57 PM, Michael Lawrence wrote: On Thu, Feb 15, 2018 at 1:45 PM, Hervé Pagès > wrote: On 02/15/2018 11:53 AM, Cook, Malcolm wrote: Hi, Can I ask, is this change under discussion in current release or so far in Biocondu

Re: [Bioc-devel] as.list of a GRanges

On Thu, Feb 15, 2018 at 1:45 PM, Hervé Pagès wrote: > On 02/15/2018 11:53 AM, Cook, Malcolm wrote: > >> Hi, >> >> Can I ask, is this change under discussion in current release or so far >> in Bioconductor devel only (my assumption)? >> > > Bioconductor devel only. > > >> > On 02/15/2018 08:37 A

Re: [Bioc-devel] as.list of a GRanges

On 02/15/2018 11:53 AM, Cook, Malcolm wrote: Hi, Can I ask, is this change under discussion in current release or so far in Bioconductor devel only (my assumption)? Bioconductor devel only. > On 02/15/2018 08:37 AM, Michael Lawrence wrote: > > So is as.list() no longer supported for GR

Re: [Bioc-devel] as.list of a GRanges

On Thu, Feb 15, 2018 at 11:53 AM, Cook, Malcolm wrote: > Hi, > > Can I ask, is this change under discussion in current release or so far in > Bioconductor devel only (my assumption)? > > > On 02/15/2018 08:37 AM, Michael Lawrence wrote: > > > So is as.list() no longer supported for GRanges obje

Re: [Bioc-devel] as.list of a GRanges

Hi, Can I ask, is this change under discussion in current release or so far in Bioconductor devel only (my assumption)? > On 02/15/2018 08:37 AM, Michael Lawrence wrote: > > So is as.list() no longer supported for GRanges objects? I have found it > > useful in places. > > Very few places.

Re: [Bioc-devel] as.list of a GRanges

On 02/15/2018 08:37 AM, Michael Lawrence wrote: So is as.list() no longer supported for GRanges objects? I have found it useful in places. Very few places. I found a dozen of them in the entire software repo. Now you should use as.list(as(gr, "GRangesList")) instead. as.list() was behaving inco

Re: [Bioc-devel] as.list of a GRanges

So is as.list() no longer supported for GRanges objects? I have found it useful in places. On Thu, Feb 15, 2018 at 8:30 AM, Hervé Pagès wrote: > Hi Bernat, > > Use as(gr, "GRangesList") instead of as.list() on your GRanges objects. > > Most of the times (e.g. for passing to lapply() or mclapply(

Re: [Bioc-devel] as.list of a GRanges

Hi Bernat, Use as(gr, "GRangesList") instead of as.list() on your GRanges objects. Most of the times (e.g. for passing to lapply() or mclapply()), you don't need an ordinary list, but, if you really want one, you can call as.list() on the GRangesList object returned by as(gr, "GRangesList"). Ho

Re: [Bioc-devel] os X Build Error and Java

Java 8 is installed on the Bioconductor build machines merida2:~ biocbuild$ java -version java version "1.8.0_111" Java(TM) SE Runtime Environment (build 1.8.0_111-b14) Java HotSpot(TM) 64-Bit Server VM (build 25.111-b14, mixed mode) The CRAN binaries for R3.5 are not yet available for some of th

[Bioc-devel] os X Build Error and Java

Dear all, I am the maintainer of the DaMiRseq package. For several days, my package is in ERROR status, only for merida2 (OS X 10.11.6 El Capitan / x86_64) in the devel release. I tried to trace the error back and I found out that the problem was due to the RWeka/Rwekajars packages. I contacted

[Bioc-devel] as.list of a GRanges

Hi, I'm having an error in the devel version of my package karyoploteR due to an error when converting a GRanges into a list of GRanges with "as.list". This used to be possible and it was working a few weeks ago. Am I suposed to use a different approach or is there a problem somewhere? Thank